Kepler Observations of the Three Pre-Launch Exoplanet Candidates: Discover of Two Eclipsing Binaries and a New Exoplanet

Three transiting exoplanet candidate stars were discovered in a ground-based photometric survey prior to the launch of NASA's Kepler mission. Kepler observations of them were obtained during Quarter 1 of the Kepler mission. All three stars are faint by radial velocity follow-up standards, so we have examined these candidates with regard to eliminating false positives and providing high confidence exoplanet selection. We present a first attempt to exclude false positives for this set of faint stars without high-resolution radial velocity analysis. This method of exoplanet confirmation will form a large part of the Kepler mission follow-up for Jupiter-sized exoplanet candidates orbiting faint stars. Using the Kepler light curves and pixel data, as well as medium-resolution reconnaissance spectroscopy and speckle imaging, we find that two of our candidates are binary stars. One consists of a late-F star with an early M companion, while the other is a K0 star plus a late M-dwarf/brown dwarf in a 19 day elliptical orbit. The third candidate (BOKS-1) is an r = 15 G8V star hosting a newly discovered exoplanet with a radius of 1.12 R_(Jupiter) in a 3.9 day orbit

The Burrell-Optical-Kepler-Survey (BOKS). I. Survey Description and Initial Results

We present the initial results of a 40 night contiguous ground-based campaign of time series photometric observations of a 1.39 deg^2 field located within the NASA Kepler Mission field of view. The goal of this pre-launch survey was to search for transiting extrasolar planets and to provide independent variability information of stellar sources. We have gathered a data set containing light curves of 54,687 stars from which we have created a statistical sub-sample of 13,786 stars between 14 < r < 18.5 and have statistically examined each light curve to test for variability. We present a summary of our preliminary photometric findings including the overall level and content of stellar variability in this portion of the Kepler field and give some examples of unusual variable stars found within. We present a preliminary catalog of 2,457 candidate variable stars, of which 776 show signs of periodicity. We also present three potential exoplanet candidates, all of which should be observable by the Kepler mission

<i>De novo</i> design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of 4-fold symmetrical (β/α)(8)-barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of sidechain-backbone hydrogen bonding for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical with the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has only sampled a subset of the sequence space available to the TIM-barrel fold. The ability to de novo design TIM-barrels opens new possibilities for custom-made enzymes

Form and Function: Two computational protein design studies

Proteine sind nicht nur grundlegende Bausteine unserer Zellen, sondern auch verantwortlich für die Katalyse der meisten Reaktionen die unser Leben ausmachen. Aufgrund ihres einfachen Aufbaus aus nur zwanzig verschiedenen Aminosäuren und der trotzdem hohen Variabilität in Größe, Form und Funktion sowie der gut skalierbaren Produktion in Bakterien haben Proteine aber auch ideale Voraussetzungen um gerichtet Katalysatoren für chemische Prozesse zu konstruieren. Hierbei sind besonders zwei Gebiete von Interesse: Das Design von Proteinfaltungen sowie das Design neuer Aktivitäten. Ein Teil der vorgestellten Arbeit beschäftigt sich mit dem Design eines de novo TIM-barrels, der wohl wichtigsten Faltung für Enzyme. Dieses Projekt entstand aus einer Zusammenarbeit mit Possu Huang und der Arbeitsgruppe von David Baker an der Universität Washington, Seattle. Verschiedene Designs, welche nach gemeinsam festgelegten Prinzipien von Possu Huang am Computer generiert worden waren, wurden dabei von mir charakterisiert. Eine Variante kristallisierte und lieferte eine Kristallstruktur die den Erfolg des Designs bestätigte. Diese Ergebnisse wurden Anfang des Jahres in Nature Chemical Biology publiziert. Der zweite Teil beschäftigt sich mit dem rationalen Design einer neuen enzymatischen Aktivität basierend auf der klassischen katalytischen Serintriade. Mehrere Proteinstrukturen wurden mittels Computer-gestützter Suche als mögliche Träger der Triade identifiziert und basierend darauf verschiedene Varianten mit optimierten Bindungstaschen in silico konstruiert und evaluiert. Die Konstrukte wurden im Labor hergestellt und analysiert. Eine Variante zeigte eine schwache katalytische Aktivität. Diese Variante wurde hinsichtlich Struktur und Funktion im Detail charakterisiert. Diese beiden komplementären Studien, die beide versuchen die Grenzen des Computer-gestützten Design der Form und Funktion von Proteinen zu erweitern, tragen bei zu einem besseren Verständnis von Proteinsequenz-, Struktur- und Funktionsbeziehungen

Computational protein design of ligand binding and catalysis

The vision of custom-made proteins by computation appears closer than ever. Computational methods have advanced rapidly in recent years and proteins have been designed to catalyze new reactions. A number of second-generation enzyme designs analyzed possible bottlenecks and started tackling emergent problems. Detailed experimental analysis combined with structure determination and molecular dynamics simulations as well as design optimization with directed evolution techniques have led to important insights. While ligand recognition seems to be particularly problematic, new approaches focus on this design aspect and promising improvements have been made